A member of a jihadist group sprays the slogan 'No Islam without Jihad' in Arabic on the wall at a border crossing with Turkey. Photograph: Bulent Kilic/AFP/Getty Images

As they stood outside the commandeered government building in the town of Mohassen, it was hard to distinguish Abu Khuder's men from any other brigade in the Syrian civil war, in their combat fatigues, T-shirts and beards.

But these were not average members of the Free Syrian Army. Abu Khuder and his men fight for al-Qaida. They call themselves the ghuraba'a, or "strangers", after a famous jihadi poem celebrating Osama bin Laden's time with his followers in the Afghan mountains, and they are one of a number of jihadi organisations establishing a foothold in the east of the country now that the conflict in Syria has stretched well into its second bloody year.

They try to hide their presence. "Some people are worried about carrying the [black] flags," said Abu Khuder. "They fear America will come and fight us. So we fight in secret. Why give Bashar and the west a pretext?" But their existence is common knowledge in Mohassen. Even passers-by joke with the men about car bombs and IEDs.

According to Abu Khuder, his men are working closely with the military council that commands the Free Syrian Army brigades in the region. "We meet almost every day," he said. "We have clear instructions from our [al-Qaida] leadership that if the FSA need our help we should give it. We help them with IEDs and car bombs. Our main talent is in the bombing operations." Abu Khuder's men had a lot of experience in bomb-making from Iraq and elsewhere, he added.

Abu Khuder spoke later at length. He reclined on a pile of cushions in a house in Mohassen, resting his left arm which had been hit by a sniper's bullet and was wrapped in plaster and bandages. Four teenage boys kneeled in a tight crescent in front of him, craning their necks and listening with awe. Other villagers in the room looked uneasy.

Abu Khuder had been an officer in a mechanised Syrian border force called the Camel Corps when he took up arms against the regime. He fought the security forces with a pistol and a light hunting rifle, gaining a reputation as one of the bravest and most ruthless men in Deir el-Zour province and helped to form one of the first FSA battalions.

He soon became disillusioned with what he saw as the rebel army's disorganisation and inability to strike at the regime, however. He illustrated this by describing an attempt to attack the government garrison in Mohassen. Fortified in a former textile factory behind concrete walls, sand bags, machine-gun turrets and armoured vehicles, the garrison was immune to the rebels' puny attempt at assault.

"When we attacked the base with the FSA we tried everything and failed," said Abu Khuder. "Even with around 200 men attacking from multiple fronts they couldn't injure a single government soldier and instead wasted 1.5m Syrian pounds [£14,500] on firing ammunition at the walls."

Then a group of devout and disciplined Islamist fighters in the nearby village offered to help. They summoned an expert from Damascus and after two days of work handed Abu Khuder their token of friendship: a truck rigged with two tonnes of explosives.

Two men drove the truck close to the gate of the base and detonated it remotely. The explosion was so large, Abu Khuder said, that windows and metal shutters were blown hundreds of metres, trees were ripped up by their roots and a huge crater was left in the middle of the road.

The next day the army left and the town of Mohassen was free.

"The car bomb cost us 100,000 Syrian pounds and fewer than 10 people were involved [in the operation]," he said. "Within two days of the bomb expert arriving we had it ready. We didn't waste a single bullet.

"Al-Qaida has experience in these military activities and it knows how to deal with it."

After the bombing, Abu Khuder split with the FSA and pledged allegiance to al-Qaida's organisation in Syria, the Jabhat al Nusra or Solidarity Front. He let his beard grow and adopted the religious rhetoric of a jihadi, becoming a commander of one their battalions.

"The Free Syrian Army has no rules and no military or religious order. Everything happens chaotically," he said. "Al-Qaida has a law that no one, not even the emir, can break.

"The FSA lacks the ability to plan and lacks military experience. That is what [al-Qaida] can bring. They have an organisation that all countries have acknowledged.

"In the beginning there were very few. Now, mashallah, there are immigrants joining us and bringing their experience," he told the gathered people. "Men from Yemen, Saudi, Iraq and Jordan. Yemenis are the best in their religion and discipline and the Iraqis are the worst in everything – even in religion."

At this, one man in the room – an activist in his mid-30s who did not want to be named – said: "So what are you trying to do, Abu Khuder? Are you going to start cutting off hands and make us like Saudi? Is this why we are fighting a revolution?"

"[Al-Qaida's] goal is establishing an Islamic state and not a Syrian state," he replied. "Those who fear the organisation fear the implementation of Allah's jurisdiction. If you don't commit sins there is nothing to fear."

Religious rhetoric

Religious and sectarian rhetoric has taken a leading role in the Syrian revolution from the early days. This is partly because of the need for outside funding and weapons, which are coming through well-established Muslim networks, and partly because religion provides a useful rallying cry for fighters, with promises of martyrdom and redemption.

Almost every rebel brigade has adopted a Sunni religious name with rhetoric exalting jihad and martyrdom, even when the brigades are run by secular commanders and manned by fighters who barely pray.

"Religion is a major rallying force in this revolution – look at Ara'our [a rabid sectarian preacher], he is hysterical and we don't like him but he offers unquestionable support to the fighters and they need it," the activist said later.

Another FSA commander in Deir el-Zour city explained the role of religion in the uprising: "Religion is the best way to impose discipline. Even if the fighter is not religious he can't disobey a religious order in battle."

Al-Qaida has existed in this parched region of eastern Syria, where the desert and the tribes straddle the border with Iraq, for almost a decade.

During the years of American occupation of Iraq, Deir el-Zour became the gateway through which thousands of foreign jihadis flooded to fight the holy war. Many senior insurgents took refuge from American and Iraqi government raids in the villages and deserts of Deir el-Zour.

Osama, a young jihadi from Abu Khuder's unit with a kind smile, was 17 in 2003 when the Americans invaded Iraq, he said. He ran away from home and joined the thousands of other Syrians who crossed the porous border and went to fight. Like most of those volunteers, at first he was inspired by a mixture of nationalistic and tribal allegiances, but later religion became his sole motivation.

After returning to Syria he drifted closer to the jihadi ideology. It was dangerous then, and some of his friends were imprisoned by the regime, which for years played a double game, allowing jihadis to filter across the borders to fight the Americans while at the same time keeping them tightly under control at home.

In the first months of the Syrian uprising, he joined the protesters in the street, and when some of his relatives were killed he defected and joined the Free Syrian Army.

"I decided to join the others," he said. "But then I became very disappointed with the FSA. When they fought they were great, but then most of the time they sat in their rooms doing nothing but smoke and gossip and chat on Skype."

Fed up with his commanders' bickering and fighting over money, he turned to another fighting group based in the village of Shahail, 50 miles west of Mohassen, which has become the de facto capital of al-Qaida in Deir el-Zour. More than 20 of its young men were killed in Iraq. In Shahail the al-Qaida fighters drive around in white SUVs with al-Qaida flags fluttering.

The group there was led by a pious man. He knew a couple of them from his time in Iraq. One day, the group's leader – a Saudi who covered his hair with a red scarf and carried a small Kalashnikov, in the style of Bin Laden – visited Mohassen. He gave a long sermon during the funeral of a local commander, telling the audience how jihad was the only way to lead a revolution against the infidel regime of Bashar al-Assad, and how they, the Syrians, were not only victims of the regime but also of the hypocrisy of the west, which refused to help them.

"They were committed," said Osama. "They obeyed their leader and never argued. In the FSA, if you have 10 people they usually split and form three groups." The jihadis, by contrast, used their time "in useful things, even the chores are divided equally".

Osama joined the group. "He [the Saudi] is a very good man, he spends his days teaching us. You ask him anything and he will answer you with verses from the Qur'an, you want to read the Qur'an you can read. You want to study bomb-making he will teach you."

In the pre-revolutionary days when the regime was strong it would take a year to recruit someone to the secret cause of jihad. "Now, thanks to God, we are working in the open and many people are joining in," said Osama.

In Shahail we interviewed Saleem Abu Yassir, a village elder and the commander of the local FSA brigade. He sat in a room filled with tribal fighters and machine-guns. The relationship with al-Qaida had been very difficult, he said, with the jihadis being secretive and despising the FSA and even calling them infidel secularists. But now they had opened up, co-operating with other rebel groups.

"Are they good fighters?" he threw the question rhetorically into the room. "Yes, they are, but they have a problem with executions. They capture a soldier and they put a pistol to his head and shoot him. We have religious courts and we have to try people before executing them. This abundance of killing is what we fear. We fear they are trying to bring us back to the days of Iraq and we have seen what that achieved."

Osama had told me that his group was very cautious about not repeating the Iraq experience – "they admit they made a lot of mistakes in Iraq and they are keen to avoid it", he said – but others, including a young doctor working for the revolution, were not convinced. The opposition needed to admit Al-Qaida were among them, and be on their guard.

"Who kidnapped the foreign engineers who worked in the nearby oilfield?" he asked. "They have better financing than the FSA and we have to admit they are here.

"They are stealing the revolution from us and they are working for the day that comes after."